Tutorial 1: Importing the XylE example

Prerequisites

A copy of the XylE example data can be found in the repository in example_data/XylE_cluster_example.csv.

Importing Data

1. Browse to XylE_cluster_example.csv. XYLE_ECOLI will automatically be selected.
2. Set State A to the wild-type/reference state by selecting XylE WT
3. Set State B to the mutant/changed state by selecting XylE E397Q
4. Enter the residue range 1 and 491 into the Residues boxes.
5. Press Import to start processing.

Note: State B should always be set to the perturbed state, otherwise differential comparisons will be the wrong way around!

The above uiwindow will appear to show what Deuteros is doing. This step might take up to 30 seconds to complete.

During import, a number of warning boxes might appear depending on the data in your cluster file. These are not errors, but let the user know what has happened to their data during processing to improve transparency.

The 154 peptides were removed error above indicates that 154 datapoints were removed. This value can be large as a "datapoint" here refers to any replicate, charge state or "peptide-timepoint" (MNTQY at 5s and 30s are two unique datapoints, for example). As both states were selected during import, any charge states/peptide-timepoints which are not common between both states would need to be removed before any downstream comparison. As the warning states, any removed datapoints can be found within the Removed Peptides table in the Data Tables tab. The Reason column of the table will display what the reason for removal:

Following successful data import, the Deuteros GUI should look like this: